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- PDB-7nos: Crystal structure of Mycobacterium tuberculosis ArgF in complex w... -

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Basic information

Entry
Database: PDB / ID: 7nos
TitleCrystal structure of Mycobacterium tuberculosis ArgF in complex with 4-bromo-6-(trifluoromethyl)-1H-benzo[d]imidazole.
ComponentsOrnithine carbamoyltransferaseOrnithine transcarbamylase
KeywordsTRANSFERASE / ArgF / Ornithine Carbamoyltransferase
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / arginine biosynthetic process via ornithine / arginine biosynthetic process / amino acid binding / cytoplasm
Similarity search - Function
Ornithine carbamoyltransferase / Ornithine/putrescine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
Similarity search - Domain/homology
PHOSPHATE ION / Chem-UJZ / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
AuthorsMendes, V. / Gupta, P. / Burgess, A. / Sebastian-Perez, V. / Cattermole, E. / Meghir, C. / Blundell, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1158806 United States
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis
Authors: Gupta, P. / Thomas, S.E. / Zaidan, S.A. / Pasillas, M.A. / Cory-Wright, J. / Sebastian-Perez, V. / Burgess, A. / Cattermole, E. / Meghir, C. / Abell, C. / Coyne, A.G. / Jacobs, W.R. / ...Authors: Gupta, P. / Thomas, S.E. / Zaidan, S.A. / Pasillas, M.A. / Cory-Wright, J. / Sebastian-Perez, V. / Burgess, A. / Cattermole, E. / Meghir, C. / Abell, C. / Coyne, A.G. / Jacobs, W.R. / Blundell, T.L. / Tiwari, S. / Mendes, V.
History
DepositionFeb 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
C: Ornithine carbamoyltransferase
D: Ornithine carbamoyltransferase
E: Ornithine carbamoyltransferase
F: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,80517
Polymers199,2506
Non-polymers1,55511
Water21,6721203
1
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
C: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3659
Polymers99,6253
Non-polymers7406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-58 kcal/mol
Surface area31460 Å2
MethodPISA
2
D: Ornithine carbamoyltransferase
E: Ornithine carbamoyltransferase
F: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4408
Polymers99,6253
Non-polymers8155
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-42 kcal/mol
Surface area31120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.995, 143.606, 97.815
Angle α, β, γ (deg.)90.000, 117.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ornithine carbamoyltransferase / Ornithine transcarbamylase / OTCase


Mass: 33208.324 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: argF, Rv1656, MTCY06H11.21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIT9, ornithine carbamoyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-UJZ / 4-bromanyl-6-(trifluoromethyl)-1~{H}-benzimidazole


Mass: 265.030 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H4BrF3N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 150 mM ammonium dihydrogen phosphate 10 mM praseodymium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.77→81.61 Å / Num. obs: 219906 / % possible obs: 100 % / Redundancy: 5.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.024 / Rrim(I) all: 0.055 / Net I/σ(I): 15.5 / Num. measured all: 1170700 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.77-1.865.31.274168321320440.5510.611.4171.1100
5.58-81.615.10.0243614970900.9990.0110.02753.999.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.03 Å81.61 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimless0.7.1data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P2G

2p2g


Resolution: 1.77→53.91 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1919 10795 4.91 %
Rwork0.1698 209045 -
obs0.1709 219840 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.59 Å2 / Biso mean: 41.7507 Å2 / Biso min: 23.1 Å2
Refinement stepCycle: final / Resolution: 1.77→53.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13589 0 82 1203 14874
Biso mean--63.8 48.45 -
Num. residues----1807
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.77-1.790.343210.319669797300
1.79-1.810.32743390.292469827321
1.81-1.830.29873500.267569727322
1.83-1.850.2753300.249669737303
1.85-1.880.24863350.240469677302
1.88-1.90.26993760.239868997275
1.9-1.930.27373530.250670007353
1.93-1.960.26473670.23770047371
1.96-1.990.26053460.219268947240
1.99-2.020.25383400.201969847324
2.02-2.060.22093220.193269957317
2.06-2.090.20293440.184869877331
2.09-2.130.21373750.179869277302
2.13-2.180.21524160.171868977313
2.18-2.220.20643350.173669887323
2.22-2.280.20663720.178669367308
2.28-2.330.22464000.177969267326
2.33-2.40.20963830.17669417324
2.4-2.470.20013810.174169417322
2.47-2.550.20183770.171769357312
2.55-2.640.19993710.165769907361
2.64-2.740.17933860.16769117297
2.74-2.870.20433540.175870117365
2.87-3.020.18853080.169169747282
3.02-3.210.19024200.168869517371
3.21-3.460.17934250.16268947319
3.46-3.80.17273710.160970187389
3.8-4.350.15312570.137571057362
4.35-5.490.15513830.144569887371
5.49-53.910.18673580.167970767434
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4666-0.63-0.46521.07790.3720.5891-0.0108-0.00030.02560.01150.0223-0.0004-0.07640.0412-00.2509-0.0173-0.00160.3074-0.01740.28810.2552-4.6083-42.0205
20.408-0.53920.38360.8325-0.39880.19560.11150.17930.081-0.3175-0.1451-0.0985-0.1219-0.0137-0.00050.38540.02720.02910.39480.01220.3148-2.44253.1468-56.3969
30.7227-0.0007-0.36021.1190.4610.8033-0.08470.0019-0.0575-0.08660.1084-0.13350.03870.116800.2204-0.00920.01930.3479-0.02860.30713.2025-17.5447-49.7487
40.6627-0.2166-0.69321.2048-0.27240.8397-0.1927-0.0195-0.12310.05680.06230.02690.2375-0.0445-0.00050.2229-0.03020.01960.2926-0.02270.28914.0886-23.0189-48.8395
51.30860.1330.09121.24680.17820.7036-0.042-0.069-0.12270.0923-0.05510.16910.1119-0.0355-00.2654-0.02230.0340.3056-0.02260.3429-28.3028-15.4757-37.4287
60.44530.07510.10980.26740.13750.069-0.06590.1411-0.0579-0.13430.02680.1752-0.17220.097-0.00010.2419-0.0239-0.01230.3415-0.03310.3244-19.6619-11.3494-48.9685
71.11650.59990.75041.24040.57430.7124-0.00070.1514-0.2906-0.0198-0.13670.31970.1044-0.0526-0.08480.2245-0.02960.00440.3493-0.10970.4926-38.1555-22.6123-48.1146
80.76970.40740.48991.04630.84470.4867-0.2002-0.08970.01010.0745-0.13170.5589-0.2333-0.1104-0.14870.13320.0221-0.06760.3331-0.09940.5312-43.2682-10.6032-47.5315
90.8459-0.2065-0.20341.241-0.49521.31260.0140.0282-0.03720.0023-0.0890.0876-0.1369-0.043-00.3040.0154-0.03250.3112-0.02390.2863-22.034314.0055-47.7453
100.1835-0.1111-0.10240.3193-0.04340.0898-0.08270.06220.0822-0.2889-0.02620.14740.0934-0.090200.4346-0.0446-0.08920.3489-0.02170.4199-31.3354-0.783-54.3012
110.87810.3137-0.42070.8636-0.47011.6707-0.03590.12770.0599-0.19490.04740.0804-0.2002-0.1858-0.00010.44160.0304-0.09020.3406-0.01070.2923-23.918522.704-61.2305
120.6123-0.31630.3770.2487-0.43670.58250.13040.1709-0.0342-0.00610.02830.0141-0.11690.0204-00.534-0.0389-0.02960.39920.02690.3056-13.575121.7092-74.5466
130.32760.0629-0.02890.2346-0.2780.5569-0.01180.1021-0.026-0.1347-0.05070.0042-0.17910.2638-0.00010.4835-0.0657-0.01480.41360.02350.326-4.480724.5641-65.9729
140.19890.04290.30920.44-0.13170.38650.14970.05440.10250.0401-0.04450.0399-0.27840.01060.00010.33150.0189-0.03960.3041-0.00780.2969-18.739617.1551-48.2269
151.0575-0.4501-0.08240.9663-0.09360.6033-0.02520.10240.05630.06890.0544-0.0014-0.08650.06010.00010.31320.01810.010.31150.01870.2826-21.777123.7364-23.5463
160.27820.0394-0.10820.3210.04860.0246-0.1167-0.1621-0.02950.42680.13480.12730.18440.11460.00010.47540.0850.00280.36550.00460.3084-16.825917.0182-11.2295
170.8916-0.74640.03750.8945-0.21380.1366-0.0307-0.10120.14160.28420.1141-0.0345-0.1162-0.028-00.4110.0601-0.00530.319-0.00990.3106-22.426529.1181-15.1637
181.5649-0.4403-0.42220.87950.35770.534-0.0994-0.12990.04110.22050.15390.1311-0.03770.0329-00.39290.08790.08450.29710.06040.3113-37.201932.4173-12.632
190.66510.02570.15761.1019-0.85711.4468-0.05110.0758-0.0139-0.0533-0.0622-0.10670.018-0.1977-00.3293-0.01670.02210.3117-0.00490.2963-26.9035-6.2385-13.17
200.23450.0022-0.19760.4346-0.18960.1267-0.01450.0776-0.14520.3290.04320.0921-0.3383-0.13290.00020.55230.10640.05140.33630.06480.3432-31.983310.8698-8.0288
210.2714-0.0141-0.22230.8682-1.01921.8964-0.04650.0385-0.00370.03170.02210.04080.0843-0.365300.3469-0.0450.04340.3497-0.01820.3227-32.3939-13.5107-0.6164
221.03890.2831-0.03880.5292-0.73021.7354-0.0991-0.1085-0.073-0.0151-0.091-0.1050.38760.1388-0.00020.43760.00550.06630.29010.01990.3666-19.6236-21.96878.4867
230.22480.1181-0.29080.1531-0.27040.348-0.0092-0.17780.1103-0.2196-0.0205-0.14430.2988-0.2431-0.00020.3308-0.03790.03110.3355-0.00480.3249-24.7685-10.325-12.7035
241.04890.40530.520.98440.48930.9572-0.04620.0552-0.03310.05190.03620.0017-0.0511-0.02970.00010.3239-0.0101-0.00050.26490.0040.28990.73743.8666-16.5726
251.23730.4586-0.16530.29090.19240.62370.0472-0.1677-0.03870.1779-0.0596-0.0031-0.0547-0.0036-00.4035-0.0355-0.02050.32910.02440.3121-0.48751.2746-6.2507
261.1293-0.19230.97540.68730.15740.9886-0.1120.0147-0.10050.16630.0664-0.2042-0.14580.1432-0.00480.4612-0.0814-0.09280.37430.00180.364719.427815.0256-4.8165
270.98630.07970.53640.6472-0.25680.8654-0.1670.06870.05680.00170.0184-0.0362-0.31520.0076-0.00270.4109-0.0457-0.04710.27950.00520.28538.817919.5561-13.3517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 64 )A0 - 64
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 114 )A65 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 231 )A115 - 231
4X-RAY DIFFRACTION4chain 'A' and (resid 232 through 307 )A232 - 307
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 50 )B1 - 50
6X-RAY DIFFRACTION6chain 'B' and (resid 51 through 84 )B51 - 84
7X-RAY DIFFRACTION7chain 'B' and (resid 85 through 245 )B85 - 245
8X-RAY DIFFRACTION8chain 'B' and (resid 246 through 307 )B246 - 307
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 64 )C1 - 64
10X-RAY DIFFRACTION10chain 'C' and (resid 65 through 94 )C65 - 94
11X-RAY DIFFRACTION11chain 'C' and (resid 95 through 208 )C95 - 208
12X-RAY DIFFRACTION12chain 'C' and (resid 209 through 245 )C209 - 245
13X-RAY DIFFRACTION13chain 'C' and (resid 246 through 284 )C246 - 284
14X-RAY DIFFRACTION14chain 'C' and (resid 285 through 307 )C285 - 307
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 50 )D1 - 50
16X-RAY DIFFRACTION16chain 'D' and (resid 51 through 83 )D51 - 83
17X-RAY DIFFRACTION17chain 'D' and (resid 84 through 159 )D84 - 159
18X-RAY DIFFRACTION18chain 'D' and (resid 160 through 307 )D160 - 307
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 64 )E1 - 64
20X-RAY DIFFRACTION20chain 'E' and (resid 65 through 94 )E65 - 94
21X-RAY DIFFRACTION21chain 'E' and (resid 95 through 201 )E95 - 201
22X-RAY DIFFRACTION22chain 'E' and (resid 202 through 284 )E202 - 284
23X-RAY DIFFRACTION23chain 'E' and (resid 285 through 307 )E285 - 307
24X-RAY DIFFRACTION24chain 'F' and (resid 0 through 64 )F0 - 64
25X-RAY DIFFRACTION25chain 'F' and (resid 65 through 143 )F65 - 143
26X-RAY DIFFRACTION26chain 'F' and (resid 144 through 245 )F144 - 245
27X-RAY DIFFRACTION27chain 'F' and (resid 246 through 307 )F246 - 307

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